HsaINT0155886 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241989234-241991277:+
Coord C1 exon
chr2:241989234-241989350
Coord A exon
chr2:241989351-241991160
Coord C2 exon
chr2:241991161-241991277
Length
1810 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
CTCTCTGTCCTTCCACACAGCCC
3' ss Score
10.99
Exon sequences
Seq C1 exon
CCCTGCCATCACCCTGCGACTCGGACCCCTGCTTCAACGGAGGCTCCTGCGATGCCCATGACGACTCCTACACCTGCGAGTGCCCGCGCGGGTTCCACGGCAAGCACTGCGAGAAAG
Seq A exon
GTATGGCGGGCAGGGGCGTCCGGGCCGGCGTCAGCACCCTGGAGAGCGCCCGCGGTCCGCCGTCCTGCTTCTCTGCTGTCTCTCTCCTTGTTTCGCGAATTGCTGACCTCGTCTAGAGCCTTGCCTGATGTGCTGCTCTGTTCTGTGTATTTAGAGGTGAGCACCTCACTGTTTGGATGGTTCTGATCTGCACCAGTGCCAGGCCTGCTGGTCATTACCTTGCTCTTCTGAAAATAGGCTTCATTGCCTGCTCAGCATTTTTCCAAATAGATTTTAGAATCATTATATCAAATTTTATTTTTAAAATTTCCATAGGATTTTGCTCAATCTAATTCAGCATGGAAAATGTCGAATTTTATTACATTTAGTCGCTTGAGAATAGAAGTGTCCTTCTGTAAGCACACTGCAGGCGTAGCTATCCCCGCCAGGCCCCACCCAGGACTGTCCCTTCTGTGCAGTTTGAAGCAACAGTCAGGACTCCCATCAGTCACCCCCAGACCTGTTCAGCATCTCAGTGGTCAGTGCCCAGAGGGGGCTGCCTGACCGCAGAGTGACCTGGCACCCTCTCCAGGGGCTCAGCCCCAGGCACCCCCGCAGCCTGGACTGGTGTGGAGCCTTCCACGGCCCCTCCCCTGCTCTGTTCCTTGTCCCTGAGGGAAAGACCCTGAAGTCTGAGCCCTGGACCCCGTGGCTCCCCCAACCACTGCAGCAGAGGTAGAACAGGTTTCCAAAGAGAAGACCCCAACTGCTTGGTTCTTTGCAAGCTCTGACGAGGTCTTTGTCTCTCAACACACTCCTAGGACCACCCTGAGGCCCTTCATGGGCCCTGCCCAGAGCTGACTCTGGCCCTACTCCAGCTCACACCTGCCAGTGGTATGAAGTCCACTGTACCCAAGGTGGGGGTCCTACCAGAGCCCACATCTCCTCACTAGACCAGACTGCTGGTACCCAGTGTCCCTGCCCCAAAGGTTCTGTGCCCGCCCCAGGAACTGCACAGCCCTCCCCCAGCATCCCAGCTTCCGTGAGCACACAGGCCACCAATGTGGACACCTCTGACCCCGGAGGGAGTACGGAAGGGACAAGGATGGCTGTCCTCAGGGGTGGGGCAGCCAGAGCTTGGACCTGCAGCGTGGGATGGCTGGCAGGAGAGGAGCGAGCACAGTGGGGCAGGCCCCTCCCGCCACTCAGAACACCCAGGGGTCCAAGGATTCGGCACTCCTCACTGGCCCTTTGACAGTGTGATTGTCAAGGTGGCAGGACAGATGTGCTTGGTTTCGCAGACACCTTTAAATATGTGCTTGCCTCAAGCACAGGCCCGGCCGTCTGAGCTCCTCGGGTTCCAGGAACTGTTAGGACCCAGGGAAAATGTGGCAATGCCAATGCAGGTACAGAACACACAGAAATCCAGATTGACTGCTGGGGACCCTGATGTCACGGCAGATGAGACTCAGCTGCTTCCTGTCAGATGGGGAATGCCCGTGTGCAGGAGGGAGGGAGTGCTGCGCCCGCTGCAGTGTTGGGGCCGGTTCTCCACAGGAAGGGCCCAGCCATTGCCAGAGCCTGGGCAGAAAAGAGGACAGGCAAGCAAAGGGCCCACCTGTGACTGAGTTGGGGTCTCCAGCCTGTGAGCCCCACCCCAGCCCCCACCATGTGTGCGGACCTGCTTGGCCCCTGCTGCAGCCAGGCCCCAGGGCTTCGTCGAGAAGGCCCCACCAGCACCAGAGGACTGAGGAGATGCCAGGAGGGTATAGTGGCTCTGTGGGGCCAGCAGCCTGGCCCCGTTCATCTGCCTCTCTGTCCTTCCACACAG
Seq C2 exon
CCCGGCCACACCTGTGCAGCTCAGGGCCCTGCCGGAACGGGGGCACGTGCAAGGAGGCGGGCGGCGAGTACCACTGCAGCTGCCCCTACCGCTTCACTGGGAGGCACTGTGAGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.002 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=PD(15.4=15.0),PF0000822=EGF=WD(100=77.5)
A:
NA
C2:
PF0000822=EGF=WD(100=77.5)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCATCACCCTGCGAC
R:
GATCTCACAGTGCCTCCCAGT
Band lengths:
231-2041
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)